Mesenchymal stem cells' differentiation into several lineages is coordinated by a complex of transcription factors and co-regulators which bind to specific gene promoters. We identified the Chromatin-Related Mesenchymal Modulator, CHD9, and demonstrated in vitro its ability for remodeling activity to reposition nucleosomes in an ATP-dependent manner. The remodeler binds to modified H3-K9me2/3 and K27me3. Little is known about CHD9 function in polymerase specific function. We showed that a new form, the nucleolar CHD9 (n-CHD9), is dynamically associated with Pol I, fibrillarin, and upstream binding factor (UBF) in the nucleoli, and functions in RNA Polymerase I (Pol I) related transcription of the ribosomal locus. Inhibitors of transcription disorganize the nucleolar compartment of transcription sites where rDNA is actively transcribed. These findings link n-CHD9 with RNA pol I transcription in fibrillar centers. Using chromatin immunoprecipitation (ChIP) and tilling arrays (ChIP-chip), we found an association of n-CHD9 with Pol I related to rRNA biogenesis. Our findings support the role for CHD9 in chromatin regulation and association with rDNA genes, in addition to its already known function in transcription control of tissue specific genes.